Dear all,
I'm going to do RNASeq on a eukaryote including the prokaryotes which populate it (skin, digestive tract etc.). I am wondering about the numbers of transcripts one has to expect coming from the different organisms when going into an experiment like this, I could not find any numbers anywhere.
There are a couple of factors which may play a role, like what exact eukaryotic host one looks at etc.pp. E.g., for a typical human, it has been reported that the number of cells from colonising organisms (mostly bacteria) outnumbers the number of cells from the human host by a factor of 10 to 1. Then again, the human genome is approximately 500 to 1000 times larger (leading to more transcription opportunities), cells are larger (more space for transcripts to persist), etc.pp
So, as a thought experiment: if we'd take a complete human, flash freeze it, grind, homogenise, extract RNA from the whole mixture and sequence that ... what would be the ratio of bacterial vs. human transcripts? Any ideas?
Best,
B.
PS: just in case it's not obvious: I am of course not doing this with human or any other higher eukaryote
I'm going to do RNASeq on a eukaryote including the prokaryotes which populate it (skin, digestive tract etc.). I am wondering about the numbers of transcripts one has to expect coming from the different organisms when going into an experiment like this, I could not find any numbers anywhere.
There are a couple of factors which may play a role, like what exact eukaryotic host one looks at etc.pp. E.g., for a typical human, it has been reported that the number of cells from colonising organisms (mostly bacteria) outnumbers the number of cells from the human host by a factor of 10 to 1. Then again, the human genome is approximately 500 to 1000 times larger (leading to more transcription opportunities), cells are larger (more space for transcripts to persist), etc.pp
So, as a thought experiment: if we'd take a complete human, flash freeze it, grind, homogenise, extract RNA from the whole mixture and sequence that ... what would be the ratio of bacterial vs. human transcripts? Any ideas?
Best,
B.
PS: just in case it's not obvious: I am of course not doing this with human or any other higher eukaryote
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